DNA origami 2.0

Agarwal, Nayan P.; Gopinath, Ashwin

doi:10.1101/2022.12.29.522100

Cited by 3 publications

(4 citation statements)

References 63 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…However, the highly attractive possibility of also retaining the site‐specific addressability of DNA nanostructures for precise guest molecule placement after biomineralization has thus far seldom been explored and has only recently been suggested for polyethylene glycol‐linkers. [ 12 ] However, in this work we show that, surprisingly, after silicification, single stranded (ss) handles of DNA or peptide nucleic acids (PNA) protruding from a DNA nanostructure remain accessible for hybridization and further functionalization. Using initially simple hybridization experiments with fluorescently labeled oligonucleotides ( Scheme a) or DNA‐coated gold nanoparticles (Au NPs) (Figure S7, Supporting Information) for structures silicified in solution (thin silica shell) followed by DNA‐PAINT super‐resolution microscopy (Scheme 1b) analysis of structures silicified on a surface (thick silica shell), we show that independent of the silicification method or thickness of the silica layer, structures remain fully site‐specifically addressable.…”

Section: Introductionmentioning

confidence: 97%

Full Site‐Specific Addressability in DNA Origami‐Templated Silica Nanostructures

et al. 2023

View full text Add to dashboard Cite

DNA nanotechnology allows for the fabrication of nanometer‐sized objects with high precision and selective addressability as a result of the programmable hybridization of complementary DNA strands. Such structures can template the formation of other materials, including metals and complex silica nanostructures, where the silica shell simultaneously acts to protect the DNA from external detrimental factors. However, the formation of silica nanostructures with site‐specific addressability has thus far not been explored. Here, it is shown that silica nanostructures templated by DNA origami remain addressable for post silicification modification with guest molecules even if the silica shell measures several nm in thickness. The conjugation of fluorescently labeled oligonucleotides is used to different silicified DNA origami structures carrying a complementary ssDNA handle as well as DNA‐PAINT super‐resolution imaging to show that ssDNA handles remain unsilicified and thus ensure retained addressability. It is also demonstrated that not only handles, but also ssDNA scaffold segments within a DNA origami nanostructure remain accessible, allowing for the formation of dynamic silica nanostructures. Finally, the power of this approach is demonstrated by forming 3D DNA origami crystals from silicified monomers. These results thus present a fully site‐specifically addressable silica nanostructure with complete control over size and shape.

show abstract

Section: Introductionmentioning

confidence: 97%

Full Site‐Specific Addressability in DNA Origami‐Templated Silica Nanostructures

et al. 2023

View full text Add to dashboard Cite

show abstract

“…Finally, we also tested our lyophilization procedure on silicified DNA origami samples. DNA origami-templated silica nanostructures have recently gained more and more attention due to their excellent combination of properties of both the DNA origami and the inorganic silica component. ,,,− They could present excellent candidates for in vivo applications due to their high stability and excellent biocompatibility. Therefore, the ability to form such structures and store them at high concentrations without an onset of aggregation is highly desirable.…”

Section: Resultsmentioning

confidence: 99%

Lyophilization Reduces Aggregation of Three-Dimensional DNA Origami at High Concentrations

Baptist

Heuer‐Jungemann

2023

ACS Omega

View full text Add to dashboard Cite

Although for many purposes, low concentrations of DNA origami are sufficient, certain applications such as cryo electron microscopy, measurements involving small-angle X-ray scattering, or in vivo applications require high DNA origami concentrations of >200 nM. This is achievable by ultrafiltration or polyethylene glycol precipitation but often at the expense of increasing structural aggregation due to prolonged centrifugation and final redispersion in low buffer volumes. Here, we show that lyophilization and subsequent redispersion in low buffer volumes can achieve high concentrations of DNA origami while drastically reducing aggregation due to initially very low DNA origami concentrations in low salt buffers. We demonstrate this for four structurally different types of three-dimensional DNA origami. All of these structures exhibit different aggregation behaviors at high concentrations (tip-to-tip stacking, side-to-side binding, or structural interlocking), which can be drastically reduced by dispersion in larger volumes of a low salt buffer and subsequent lyophilization. Finally, we show that this procedure can also be applied to silicified DNA origami to achieve high concentrations with low aggregation. We thus find that lyophilization is not only a tool for long-term storage of biomolecules but also an excellent way for up-concentrating while maintaining well-dispersed solutions of DNA origami.

show abstract

“…Minimizing the TEOS cross-reaction between silica shells during silicification should allow for more robust silica growth and improved tunability of the shell thickness. Recently, it was shown that thicker silica growth could be achieved by coating DNA origami with poly(ethylene glycol)- b -poly( l -lysine) block copolymers via electrostatic adsorption . We therefore hypothesize that a protective “shield” of long DNA strands on the origami surface can effectively prevent the origami cores (where we believe most of the silica growth occurs) from touching and reacting with each other.…”

Section: Introductionmentioning

confidence: 94%

“…Recently, it was shown that thicker silica growth could be achieved by coating DNA origami with poly(ethylene glycol)-b-poly(L-lysine) block copolymers via electrostatic adsorption. 29 We therefore hypothesize that a protective "shield" of long DNA strands on the origami surface can effectively prevent the origami cores (where we believe most of the silica growth occurs) from touching and reacting with each other. To achieve this, we turned to a surface-initiated terminal deoxynucleotidyl transferase (TdT) polymerization reaction on DNA origami that we have recently developed.…”

Section: ■ Introductionmentioning

confidence: 99%

Controlling Silicification on DNA Origami with Polynucleotide Brushes

Wang,

Lin,

DeLuca

et al. 2023

J. Am. Chem. Soc.

View full text Add to dashboard Cite

DNA origami has been used as biotemplates for growing a range of inorganic materials to create novel organic− inorganic hybrid nanomaterials. Recently, the solution-based silicification of DNA has been used to grow thin silica shells on DNA origami. However, the silicification reaction is sensitive to the reaction conditions and often results in uncontrolled DNA origami aggregation, especially when growth of thicker silica layers is desired. Here, we investigated how site-specifically placed polynucleotide brushes influence the silicification of DNA origami. Our experiments showed that long DNA brushes, in the form of single-or double-stranded DNA, significantly suppress the aggregation of DNA origami during the silicification process. Furthermore, we found that double-stranded DNA brushes selectively promote silica growth on DNA origami surfaces. These observations were supported and explained by coarsegrained molecular dynamics simulations. This work provides new insights into our understanding of the silicification process on DNA and provides a powerful toolset for the development of novel DNA-based organic−inorganic nanomaterials.

show abstract

DNA origami 2.0

Cited by 3 publications

References 63 publications

Full Site‐Specific Addressability in DNA Origami‐Templated Silica Nanostructures

Full Site‐Specific Addressability in DNA Origami‐Templated Silica Nanostructures

Lyophilization Reduces Aggregation of Three-Dimensional DNA Origami at High Concentrations

Controlling Silicification on DNA Origami with Polynucleotide Brushes

Contact Info

Product

Resources

About